9:5 So when the sacred months have passed, then slay the polytheists wherever you find them, and capture them, and besiege them, and lie in wait for them at every ambush. But if they repent and keep up the Salat and pay the Zakat, then leave them alone on their path. Surely Allah is most Forgiving, most Rewarding.

9:5 Regarding the significance of sacred months see notes to v. 2. Many malicious critics of Islam fully exploited the outward message of the verse to project a seriously distorted picture of Islam and concluded its militant stance is the cause behind many of the hostilities in the world. Their basic analogy is how this religion, bearing a name of peace, could teach killing innocent people. The critics try to portray every Muslim is required to slay every non-Muslim wherever they may find them, at peace time or otherwise. In this context, it is important to note that nowhere in the Qur’ān, free permission was given to kill anyone anywhere. Therefore, the message of the verse must be objectively analyzed and interpreted in context of the revelation and its application must be done in circumstances similar to that necessitated the revelation.
Regardless of the name or intent of the religion, the Qur’ān, being a complete guide for every problem at personal, communal and state level, must address what should be done if fundamental rights of a community or a nation are violated due to armed aggression and appropriate collective redress cannot be established due to lack of a system to assure peace or disinterest and/or inability of a system to solve the crisis. With or without the Qur’ānic instruction, a Muslim community or a nation is expected to react exactly the same way a non-Muslim community or a nation would react if they are attacked or war is waged against them. Only difference is a non-Muslim community or a nation would defend itself against hostile aggression or war out of their instinctive or constitutional right to protect them, without having to recourse to their scriptures. Since no other scripture claims to contain ‘complete guidance’ for mankind, it is no surprise to see they do not address complex socio-political issues of war and peace.
Before giving the permission to capture, wait in ambush or slay the unbelievers, the Qur’ān made it clear to comply with peace treaty with those who are willing to uphold it (previous verse). It must be remembered that initiative for all peace treaty was made from the Muslim side, as war was not seen as an objective of Islam. It must also be remembered that in the pre-Islamic era and during the development of Islamic era, annulment of peace treaty between two hostile tribes was nothing but declaration of open war. The Muslims were therefore, specifically instructed to fight against those tribes that annulled peace treaty. In this regard, specific notation of 2:190-193 may be made that say: and fight in the way of Allāh against those who fight with you and do not transgress. Thus, war is permissible only in self-defense, and not as an act of active aggression. While in a war Islam permits everything necessary and advisable in warfare, yet it prohibits undue aggression in war (2:190, 193; 8:39,61-62).
The malicious critics of Islam often quote the second half of the verse to imply that non-Muslims were converted into Islam with great degree of coercion. This message must be reviewed in conjunction with several other fundamental ordinances of the Qur’ān that say: there is no compulsion in religion, the Right Path has indeed been made distinct from the wrong (2:256; also see 6:105; 10:99; 18:29; 27:92; 42:15; 73:19; 76:29). Keeping this in mind, the only way the captives in war could be prevented from reverting to hostility upon their release was to make them embrace Islam. Such conversion in Islam was purely as a war strategy and should not be viewed as general approach during peacetime or as intolerance of their faith. In every age, the hostile pastors of many Churches quoted this ruling of the verse in a much generalized sense to incite hatred towards Islam.
Nowhere the verse says the captives were to be converted. Three things about the captives are stated: (a) if they repent, (b) if they keep up salāt, and (c) if they pay zakat, they should be left alone on their path. The condition of professing faith in Islam is clearly absent. Mention of salāt and zakat may have misled the critics into believing the captives were converted into Islam and then left alone. Even before the advent of Islam, the Arabs were accustomed to performing salāt and paying zakat, just as Ibrāhīm, Ismā‘īl, Mūsā, Jesus and their disciples were mandated to perform salāt and pay zakat (19:31,55; 21:73). By sincerely expressing repentance for waging war and then by showing adherence to their form of salāt and zakat, the captives would have rightly demonstrated change in their evil intentions.